Cumulative frequency bar plot of top sequences

Description

Create a cumulative frequency bar plot of a specified number of top sequences.

Usage

topSeqsPlot(list, top = 10)

Arguments

Details

The plot is made using the package ggplot2 and can be reformatted using ggplot2 functions. See examples below.

Value

Returns a cumulative frequency bar plot of the top sequences.

See Also

An excellent resource for examples on how to reformat a ggplot can be found in the R Graphics Cookbook online (http://www.cookbook-r.com/Graphs/).

Examples

file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

topSeqsPlot(list = file.list, top = 10)

# Display the number of sequences at the top of bar plot and add a title
n <- as.character(lapply(file.list, nrow))

topSeqsPlot(list = file.list, top = 10) + 
   ggplot2::annotate("text", x = 1:length(file.list), y = 105, label = n, color = "black") +
   ggplot2::expand_limits(y = c(0, 110)) + ggplot2::ggtitle("Figure Title") + 
   ggplot2::scale_x_discrete(limits = names(file.list))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(LymphoSeq)
Loading required package: LymphoSeqDB
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LymphoSeq/topSeqsPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: topSeqsPlot
> ### Title: Cumulative frequency bar plot of top sequences
> ### Aliases: topSeqsPlot
> 
> ### ** Examples
> 
> file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
> 
> file.list <- readImmunoSeq(path = file.path)
   |                                                                               |                                                                      |   0%   |                                                                               |======                                                                |   9%   |                                                                               |=============                                                         |  18%   |                                                                               |===================                                                   |  27%   |                                                                               |=========================                                             |  36%   |                                                                               |================================                                      |  45%   |                                                                               |======================================                                |  55%   |                                                                               |=============================================                         |  64%   |                                                                               |===================================================                   |  73%   |                                                                               |=========================================================             |  82%   |                                                                               |================================================================      |  91%   |                                                                               |======================================================================| 100%
> 
> topSeqsPlot(list = file.list, top = 10)
> 
> # Display the number of sequences at the top of bar plot and add a title
> n <- as.character(lapply(file.list, nrow))
> 
> topSeqsPlot(list = file.list, top = 10) + 
+    ggplot2::annotate("text", x = 1:length(file.list), y = 105, label = n, color = "black") +
+    ggplot2::expand_limits(y = c(0, 110)) + ggplot2::ggtitle("Figure Title") + 
+    ggplot2::scale_x_discrete(limits = names(file.list))
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>